Generally I found that people use an ionic detergent for sample preparation of 2-DE , so what if i use ionic detergent like Tritonx 100 for 2-DE sample preparation?
Using an ionic detergent risks introducing charged contaminants to your sample, which may disrupt the isoelectric focusing - and more importantly, may alter the observed pI of your protein(s). I have heard of people getting IEF to work with Trion-X or NP-40, but I would expect it to result in streaking.
Page 6 of this PDF may be useful: http://www.aesociety.org/areas/pdfs/Garfin_IEF_WebArticle9-07.pdf
If you need to use Triton-X, perhaps you could buffer exchange it out?
In 2-DE the first separation (isoelectric focusing) is dependent on the protein charge. Therefore any additional charges which are not linked to proteins should be minimized since they otherwise disturb the protein separation (visible as horizontal streaking in the 2D gel). Although mild ionic detergents (e.g Triton X100, NP40) have been used for IEF in the early steps of 2-DE there is a risk (dependent on their concentration) that they might have more negative effects (disturbing protein separation) than positive effects (keeping the protein unfolded). Since not all molecules of the same protein will finally bind the same amount of detergent this will cause different charged states of the same protein. Therefore the protein will not be concentrated at one specific position (isoelectric point) in the pH gradient but instead at many different positions which cause the streaking.
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